No a colonoscopy does not hurt abd is nothing to dread. The standard procedure is to sedate you with demerol and an amnesiac drug (usually valium, versed or propofol) which puts you into a twilight sleep and makes you remember none of it . . . though it is possible to have the exam with no sedation at all (as I have done) and experience discomfort on the level of bad gas pains. The interior walls of the GI tract have no sensory nerve endings so biopsies and polyp removals are entirely painless. Really the cleanout prep is the most invonvenient part of the whole thing.
As for antibiotics, that should not interfere. However, be aware that most antibiotics kill off some fo the normal gut bacteria which can cause diarrihea. A good rule of thumb when taking antibiotics is to also take a probiotic (check at any health food store) to replace the healthy gut flora. Finally, doctors should not prescribe antibiotics for a cold, which is caused by a virus . . . only for a bacterial infection which can sometimes follow a cold.